Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in (Q41915155)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19754142%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

title

Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19754142%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

0 references

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19754142%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

Nils G Walter

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19754142%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

Mark A Ditzler

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19754142%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

Jirí Sponer

3

1 reference

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7 February 2020

author name string

Mark A Ditzler

1

1 reference

14 October 2017

Jirì Sponer

3

1 reference

14 October 2017

language of work or name

English

0 references

publication date

1 January 2010

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19754142%20AND%20SRC:MED&resulttype=core&format=json

Accounts of Chemical Research

7 February 2020

published in

1 reference

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7 February 2020

volume

43

1 reference

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7 February 2020

issue

1

1 reference

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7 February 2020

page(s)

40-47

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19754142%20AND%20SRC:MED&resulttype=core&format=json

Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.

7 February 2020

cites work

1 reference

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Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.

5 June 2018

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5 June 2018

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5 June 2018

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Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases

5 June 2018

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Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids

5 June 2018

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RNA dynamics: it is about time.

5 June 2018

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Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis

5 June 2018

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Control of protein synthesis and mRNA degradation by microRNAs

5 June 2018

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Towards a molecular dynamics consensus view of B-DNA flexibility

5 June 2018

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RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

5 June 2018

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Ribozyme catalysis revisited: is water involved?

5 June 2018

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Molecular dynamics simulations and their application to four-stranded DNA.

5 June 2018

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Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics

5 June 2018

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Leading RNA tertiary interactions: structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view.

5 June 2018

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Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA

5 June 2018

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Coupling of fast and slow modes in the reaction pathway of the minimal hammerhead ribozyme cleavage

5 June 2018

1 reference

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Structural roles of monovalent cations in the HDV ribozyme

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2808146

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

5 June 2018

1 reference

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The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2808146

Molecular dynamics simulations of RNA: an in silico single molecule approach.

5 June 2018

1 reference

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Trapped water molecules are essential to structural dynamics and function of a ribozyme

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2808146

Structure of ribonuclease P--a universal ribozyme.

5 June 2018

1 reference

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Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2808146

Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer

5 June 2018

1 reference

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Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn

5 June 2018

1 reference

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Mechanism of peptide bond synthesis on the ribosome

5 June 2018

1 reference

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Targeting proteins to membranes: structure of the signal recognition particle.

5 June 2018

1 reference

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Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases

5 June 2018

1 reference

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5 June 2018

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Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations

5 June 2018

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Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.

5 June 2018

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Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests

5 June 2018

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Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis

5 June 2018

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5 June 2018

Polarizable force fields

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The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

5 June 2018

1 reference

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General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2808146

Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2808146

General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility

18 August 2018

1 reference

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Simulating RNA folding kinetics on approximated energy landscapes

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2808146

Dynamics of B-DNA on the microsecond time scale.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2808146

A model for how ribosomal release factors induce peptidyl-tRNA cleavage in termination of protein synthesis.

18 August 2018

1 reference

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Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2808146

General acid catalysis by the hepatitis delta virus ribozyme

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2808146

What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome?

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2808146

Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2808146

Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations

18 August 2018

1 reference

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Density Functionals with Broad Applicability in Chemistry

18 August 2018

1 reference

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Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs

2 December 2018

1 reference

12 December 2020

Nature of Base Stacking: Reference Quantum-Chemical Stacking Energies in Ten Unique B-DNA Base-Pair Steps

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12 December 2020

Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin

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12 December 2020

The properties and functions of virus encoded microRNA, siRNA, and other small noncoding RNAs

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12 December 2020

Polarizable Force Fields: History, Test Cases, and Prospects

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12 December 2020

Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator

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12 December 2020

Identifiers

DOI

10.1021/AR900093G

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19754142%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19754142%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

PubMed publication ID

19754142

1 reference